Having finally used the Pro controller for myself (none of my friends had it) I can say that Nintendo probably just went with a controller shape that was conventional to appeal to core gamers and just like you said kept the same stick and button layout as the gamepad which is made the way it is to accommodate for left handed players.

Personally I'm glad they didn't make it like the GCN controller. This offers more options and more room for preferences between players IMO.